REU Participating Faculty
- Balu Addepalli, biochemistry, bioanalytical chemistry
- Noe Alvarez, analytical chemistry, nanomaterials
- Neil Ayres, polymer chemistry
- Tom Beck, physical, computational chemistry
- Ruxandra Dima, physical, computational chemistry (co-PI)
- Hairong Guan, inorganic & organic chemistry
- Anna Gudmundsdottir (PI), organic chemistry, material science
- In-Kwon Kim, biochemistry
- James Mack, organic chemistry, green chemistry
- Eddie Merino, biochemistry
- Ashley Ross, analytical chemistry, neuroscience
- Laura Sagle, biophysical chemistry
- Yujie Sun, inorganic, catalysts
- George Stan, physical, computational chemistry
- Ryan White, analytical chemistry
- Peng Zhang, analytical, materials chemistry
Topic: Epitranscriptomics of RNA chemical modifications
I am interested in development and demonstration of the utility of various molecular tools and technologies associated with epitranscriptomics of coding and noncoding RNA. These include development of enzymes for qualitative and quantitative determination of chemical modifications in RNA by mass spectrometry or RNA-seq type of high-throughput approaches, and development of bait molecules for isolating target RNAs from complex biological mixtures. These novel and high-throughput approaches will expand and enhance the currently available strategies for understanding the functional significance of a variety of chemical modifications in RNA nucleosides, termed as epitranscriptomics. The REU student engaged in such research studies will learn various bioanalytical and molecular biology techniques for analysis of RNA structure and function, thereby gaining experience in biochemistry and bioanalytical chemistry of RNA and proteins, their purification, and mass spectrometry. This endeavor will help the REU student in understanding the interphase of chemistry and biology associated with molecular processes of gene expression and epigenetic regulation.
The research in our group is focused on carbon nanomaterials synthesis and assembly into macroscopic materials for sensor applications. We synthesize and assemble carbon nanotubes into fibers and films and use them for physiological and electrochemical sensors, as well as energy storage devices. Besides of the fundamental chemistry such as synthesis and electrochemistry, students in the Lab are exposed to engineering aspects of nanomaterials development. We are developing microelectrodes suitable for physiological applications such as recording extracellular activity for neuroscience research and the ability to stimulate neurons in a targeted fashion. This research is focused on a bottom-up approach that allows us to combine carbon nanotubes (CNTs) into macroscopic flexible electrodes that can be adjusted to application-specific requirements. Electron transfer rates are currently under study using Electroretinogram (ERG) for signal recording and others for electrical stimulation. Biocompatible polymer coatings and control over their porosity and stiffness are topics of interest in neuroscience as implants to prevent damaging brain tissue. Additionally, we work on heavy metals detection in drinking water that has become high priority for our society, particularly for people living in cities where water infrastructure was built more than 30 years ago. This research intents to develop an electrochemical sensor based on CNTs to detect toxic metals such as Pb, Cd and Hg and can monitor them autonomously.
The use of polymers in society has become ubiquitous, from commodity items to high technology and cutting-edge therapeutics and diagnostics. The research in our group is focused on synthetic chemistry approaches to studying new biomaterials. Specifically, we are interested in blood-contacting biomaterials and co-polymer foams. To accomplish our goals, we use polymer chemistry to mimic naturally occurring biological macromolecules. In addition to uses as new biomaterials, the polymers prepared in our group can be used as shape-memory polymers, self-healing materials, gel-forming materials, and rheology modifiers. REU students in our group will contribute to using this chemistry to prepare polymers designed for determining the structure/activity relationships of synthetic heparin mimics. This project will result in a rationally designed set of materials with precise architecture and functional groups that will provide new, fundamental insights into polymer/host interactions. Students involved in this project will gain experience in polymer synthesis and characterization techniques, experimental design, and problem solving techniques.
Our research group works in the areas of theoretical and computational chemistry, employing fundamental ideas from statistical mechanics, quantum mechanics, and thermodynamics to study a range of condensed phase problems. These problems include the basic aspects of ion solvation in water and near interfaces, ions in organic solvents used in lithium ion batteries and supercapacitors, and the biophysics of ion channels. We are also developing new theoretical and computational methods to examine these problems. Several projects are available for an REU summer student: 1) molecular dynamics simulations of ions in large water clusters, 2) related simulations of ions in ethylene carbonate and propylene carbonate, and 3) theory and modeling of ions in binding sites in chloride channels and transporters. The student would gain extensive experience in modeling complicated liquids, interfacial systems, and/or proteins. The work has a direct impact on gaining a better understanding of ionic solutions, energy storage, and ion binding and transport in biological systems.
Our group is engaged in fundamental research related to the thermodynamics and kinetics of biopolymers. There are two main lines of research, both involving the study of biological assemblies whose action involves conversion of chemical energy into mechanical energy. The first direction is related to the action of molecular machines called chaperones that assist or direct the remodeling of either newly synthesized proteins or misfolded proteins due to stresses such as heat or chemical denaturation. The second direction is related to deciphering the mechanism of action of molecular motors on cytoskeletal filaments during fundamental cellular processes such as mitosis or axonal and dendrites growth. The research is directed at developing new computational approaches for modeling the mechanical response of large protein complexes under various cellular conditions, leading to fundamental insight into the role played by forces in the life of the cell. External tension is applied to cells during processes such as cell–cell adhesion, blood flow, wound closure, axonal growth, and mitosis. As a result, force-induced changes occur in cytoskeletal proteins, leading to the deformation of cells and transduction of mechanical signals into biochemical signals, ultimately inducing biological responses such as alterations in specific gene expression, changes in protein synthesis, and channel activation. A project for an REU student is "Computational modeling of the action of molecular machines during stress application in cells". The goal of this project is to determine the changes in the mechanical response of protein–protein interactions between molecular machines, such as chaperones and substrate proteins, or molecular motors, such as kinesins and cytoskeletal filaments, that allow the cell to respond and adapt to the action of mechanical forces. A student involved in this project will become familiar with the computational methodology behind realistic modeling of proteins and their cellular environment (water, ions), learn how to use visualization tools for large biomolecules, become familiar with protein databases, and gain extensive knowledge in searching the scientific literature.